Ancient war of the world within

Research by Dr. Sara Sawyer and colleagues revealed an ancient genome-defense system that now helps the body protect itself from HIV infection.

Photo by Todd Mcnaught

An unusual defense mechanism that the body uses to attack the AIDS virus evolved millions of years before the existence of HIV, according to new research from the Basic Sciences Division. The researchers suspect that this ancient form of protection originally arose to combat distantly related virus-like invaders.

The new study led by Dr. Sara Sawyer, a postdoctoral researcher in Dr. Harmit Malik's lab, focused on a recently discovered human protein known as Apobec3G. The protein defends cells from HIV infection by causing mutations in the virus' genetic material. In response, HIV produces a protein called Vif that binds to Apobec3G and targets it for destruction. Genetic tug of war battles of this kind typically put pressure on both sparring partners to continually evolve new capabilities to overcome the other.

Despite the specific nature of the Vif/Apobec3G interaction, Sawyer and colleagues found to their surprise that Apobec3G began to evolve in response to an antagonist more than 32 million years before HIV-like viruses became endemic in primates. Their conclusions are based on a comparison of human Apobec3G genes—which hold the DNA blueprint for making Apobec3G proteins—with those of man's distantly related primate relatives.

"That suggests that HIV is a newcomer to this conflict," Malik said. "The host can't evolve a completely new defense in such a short period of time."

The discovery of Apobec3G's continual evolution suggests that some forms of the protein may be more effective at overcoming HIV infection than others, which could influence whether or not a person's disease progresses, said Dr. Michael Emerman, an HIV researcher in the Human Biology and Basic Sciences divisions and a study coauthor.

"There is great variation in disease progression among HIV-infected individuals," he said. "This variability is influenced by the type of virus that infects a person as well as by the person's genetic makeup. Increasingly, human genes are being discovered that influence viral progression. Apobec3G is a good candidate to be one of these genes."

Apobec3G proteins from different species are only capable of defending against a limited range of viruses that naturally infect different primates. Therefore, Emerman said the comparative study of Apobec3G might also yield insight into the range of HIV-like strains that could potentially infect the human population.

Published on the Public Library of Science Web site, the study will appear in the journal's September print edition.

The new findings are a notable example of lessons gleaned from the study of rapidly evolving proteins, a research approach taken by Malik's lab. Conflicts in nature drive this type of evolutionary change when two competing biological interests come head to head. Predators and prey often influence the evolution of one another. Similar genetic arms races can happen between the viruses and proteins of the cells they infect.

"We don't always know what the conflict is, but by looking for proteins that are rapidly evolving in response to selective pressures we can identify candidates that participate in conflict," Malik said. "Some of them will be relevant to disease."

To hunt for rapidly evolving genes, his lab examines closely related species to identify equivalent genes from each organism. They look for those whose DNA sequences differ in significant ways among species. Some DNA sequence differences result in changes to their respective proteins that noticeably affect protein function. This suggests that an arms race might be taking place because nature has not settled on an optimal form. Once candidates are identified, the researchers must hunt for the opponent or opponents in the conflict in order to develop hypotheses to explain why the adaptive evolution is taking place.

Sawyer and Malik speculated that Apobec3G might be an example of a rapidly evolving protein after hearing a talk given by Emerman at the Basic Sciences Division retreat last fall, in which he mentioned the recently discovered defense mechanism against Vif.

"Rarely do you see such clear examples of proteins directly in conflict," Malik said. "We decided to see whether Apobec3G showed signs of rapid evolution in response to selective pressure."

Backtracking through evolution

To characterize the selective pressure on Apobec3G evolution, Sawyer and colleagues analyzed the gene from twelve primates—New World monkeys, Old World monkeys, great apes and human—spanning 33 million years of evolution. This kind of approach allows scientists to backtrack through evolution and identify both recent genetic changes as well as come up with a hypothetical ancestor of all the species.

Most of the primates they examined showed evidence of what is known as positive selection, indicating that the gene has been under pressure to evolve throughout history. But lentiviruses—the family of viruses to which HIV belongs—have been found in only some of the primates studied and appear to be at most 1 million years old.

"What is novel about our findings is that scientists tend to study evolution of viruses but not the host proteins that work against them," Sawyer said. "Based on how rapidly HIV changes, we assumed that we could learn something by focusing on Apobec3G."

The original enemy

The researchers propose that Apobec3G's original enemy is a family of virus-like invaders of the genome called retrotransposons. Known as mobile genetic elements, these snippets of DNA are thought to be relics of ancient viral infections that insert themselves selfishly into many places in the genome, regardless of whether they may disrupt the genes that inhabit those locations. HIV and other lentiviruses are similar to these ancient genetic attackers in that they also insert themselves into the host genome after infection. The new study is the first detailed examination of such a genome-defense system in which both parties to the conflict have been clearly identified.

Sawyer and colleagues conducted a similar analysis of other mutation-inducing proteins closely related to Apobec3G and found that some of them also show signs of positive selection. These too may be have arisen to defend the host genome against mobile genetic elements and may now play a role in defending humans against as yet unknown viruses.

Malik said that there is a good lesson to be learned from this type of evolutionary analysis of the genome.

"If you study what some people consider harmless oddities of the genome and the host defenses against them, you may uncover some very interesting aspects of biology that have important implications for human disease."